Locus 13531

Sequence ID dm3.chrX
Location 7,248,877 – 7,248,988
Length 111
Max. P 0.998944
window18630 window18631 window18632 window18633

overview

Window 0

Location 7,248,877 – 7,248,983
Length 106
Sequences 7
Columns 111
Reading direction forward
Mean pairwise identity 69.10
Shannon entropy 0.59372
G+C content 0.48147
Mean single sequence MFE -31.04
Consensus MFE -21.38
Energy contribution -20.09
Covariance contribution -1.30
Combinations/Pair 1.55
Mean z-score -1.88
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.06
SVM RNA-class probability 0.997246
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 7248877 106 + 22422827
--ACAUCGAAUCCUGCGGAUGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUACCCAUCCCGAAAUGGGAUGGAAACAAAAAAAAAA---AAAAUAACUGGCUAUACG
--.((((..........))))....((((........(((((........)))))..(((((((.....)))))))..............---.......))))....... ( -25.20, z-score =  -2.11, R)
>droSim1.chrX 5785560 99 + 17042790
--ACAUCGAAUCCGGCGGAUGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAA----------UAACUGGCUAUACG
--........((((.....))))..((((.......((((((........)))))).(((((((.....)))))))...........----------...))))....... ( -27.70, z-score =  -1.65, R)
>droSec1.super_24 458482 99 + 912625
--ACAUCGAAUCCCGCGGAUGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAA----------UAACUGGCUAUACG
--.((((..........))))....((((.......((((((........)))))).(((((((.....)))))))...........----------...))))....... ( -27.20, z-score =  -1.89, R)
>droYak2.chrX 7667921 91 - 21770863
----ACCGAGUCUAGCGAAUG-AGCCCAGAACUUGUGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAAAAAUGGAAA---------------
----.(((..(((.((.....-.))..)))..((((((((((........)))))).(((((((.....)))))))..))))........)))...--------------- ( -25.70, z-score =  -2.56, R)
>droEre2.scaffold_4690 16155043 107 + 18748788
----ACCGAAUCCAGCGAACGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAAAAAGAAAAAAUUACUGGCUGUACG
----...........((.((((...((((.......((((((........)))))).(((((((.....)))))))........................)))))))).)) ( -28.00, z-score =  -2.52, R)
>dp4.chrXL_group1e 11211945 111 + 12523060
AUACAGCAAAUCCGCCGGAUGGAGUCCAGAACUUGCGGUCACUGAUUCAUGCGGCCGGGGCUCUGGUCUGGGGUUCGGAUUUGGGAUACGGGUCCGUUCUUUGGAUAUGGA
......((.((((.(((((((((((((........(((((.(........).)))))))))))).))))))((..((((((((.....))))))))..))..)))).)).. ( -40.80, z-score =  -0.83, R)
>droPer1.super_14 655147 111 + 2168203
AUACAGCAAAUCCGCCGGAUGGAGUCCAGAACUUGCGGUCACUGAUUCAUGCGGCCGGGGUUCUGGUCUGGGGUUCGGAUUUGGGAUACGGGUCCGUUCUUUGGAUAUGGA
......((.((((.(((((......(((((((((.(((((.(........).)))))))))))))))))))((..((((((((.....))))))))..))..)))).)).. ( -42.70, z-score =  -1.58, R)
>consensus
__ACAUCGAAUCCGGCGGAUGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAAAAA___AAA_UAACUGGCUAUACG
..........(((.......)))..((((.......((((((........)))))).(((((((.....)))))))........................))))....... (-21.38 = -20.09 +  -1.30)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,248,877 – 7,248,983
Length 106
Sequences 7
Columns 111
Reading direction reverse
Mean pairwise identity 69.10
Shannon entropy 0.59372
G+C content 0.48147
Mean single sequence MFE -28.71
Consensus MFE -16.14
Energy contribution -16.70
Covariance contribution 0.56
Combinations/Pair 1.30
Mean z-score -1.46
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.80
SVM RNA-class probability 0.968261
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 7248877 106 - 22422827
CGUAUAGCCAGUUAUUUU---UUUUUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGUAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCAUCCGCAGGAUUCGAUGU--
......((..((((((..---(((......((..((((((((.....))))))))...))...)))..)))))).)).(((((((((......)).)))))))......-- ( -26.70, z-score =  -1.40, R)
>droSim1.chrX 5785560 99 - 17042790
CGUAUAGCCAGUUA----------UUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCAUCCGCCGGAUUCGAUGU--
..............----------.......((..(((((((.....)))))))..)).(((((((((...((.(....).)).((((...))))....))))).))))-- ( -27.30, z-score =  -0.53, R)
>droSec1.super_24 458482 99 - 912625
CGUAUAGCCAGUUA----------UUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCAUCCGCGGGAUUCGAUGU--
......((..((((----------((..(((((..(((((((.....)))))))..)).....)))..)))))).))......((((((((......))))))))....-- ( -28.80, z-score =  -0.85, R)
>droYak2.chrX 7667921 91 + 21770863
---------------UUUCCAUUUUUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCACAAGUUCUGGGCU-CAUUCGCUAGACUCGGU----
---------------...((........(((((..(((((((.....)))))))((.((((........))))))))))).(((((.(.-.....))))))...)).---- ( -25.00, z-score =  -1.45, R)
>droEre2.scaffold_4690 16155043 107 - 18748788
CGUACAGCCAGUAAUUUUUUCUUUUUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCGUUCGCUGGAUUCGGU----
((.....(((((...................((..(((((((.....)))))))..)).....(((((...((.(....).))..))))).....)))))...))..---- ( -31.60, z-score =  -2.02, R)
>dp4.chrXL_group1e 11211945 111 - 12523060
UCCAUAUCCAAAGAACGGACCCGUAUCCCAAAUCCGAACCCCAGACCAGAGCCCCGGCCGCAUGAAUCAGUGACCGCAAGUUCUGGACUCCAUCCGGCGGAUUUGCUGUAU
......(((.......)))...((((..((((((((.........(((((((..(((.(((........))).)))...)))))))...((....))))))))))..)))) ( -30.80, z-score =  -1.82, R)
>droPer1.super_14 655147 111 - 2168203
UCCAUAUCCAAAGAACGGACCCGUAUCCCAAAUCCGAACCCCAGACCAGAACCCCGGCCGCAUGAAUCAGUGACCGCAAGUUCUGGACUCCAUCCGGCGGAUUUGCUGUAU
......(((.......)))...((((..((((((((.........(((((((..(((.(((........))).)))...)))))))...((....))))))))))..)))) ( -30.80, z-score =  -2.14, R)
>consensus
CGUAUAGCCAGUUA_UUU___UUUUUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCAUCCGCCGGAUUCGAUGU__
...............................(((((((((((.....)))))))))))....((((((...((.(....).)).(((.....)))....))))))...... (-16.14 = -16.70 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,248,881 – 7,248,988
Length 107
Sequences 7
Columns 112
Reading direction forward
Mean pairwise identity 66.93
Shannon entropy 0.63868
G+C content 0.47428
Mean single sequence MFE -32.31
Consensus MFE -18.73
Energy contribution -17.03
Covariance contribution -1.70
Combinations/Pair 1.62
Mean z-score -2.24
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.56
SVM RNA-class probability 0.998944
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 7248881 107 + 22422827
CGAAUCCUGCGGAUGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUACCCAUCCCGAAAUGGGAUGGAAACAAAAAAAAAAAAAAUAACUGGCUAUACGUAUAA-----
.......((((.((((...((((........(((((........)))))..(((((((.....))))))).....................)))))))).))))...----- ( -28.00, z-score =  -3.07, R)
>droSim1.chrX 5785564 100 + 17042790
CGAAUCCGGCGGAUGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAA-------UAACUGGCUAUACGUAUAA-----
........(((.((((...((((.......((((((........)))))).(((((((.....)))))))...........-------...)))))))).)))....----- ( -29.40, z-score =  -2.19, R)
>droSec1.super_24 458486 100 + 912625
CGAAUCCCGCGGAUGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAA-------UAACUGGCUAUACGUACAA-----
........(((.((((...((((.......((((((........)))))).(((((((.....)))))))...........-------...)))))))).)))....----- ( -29.30, z-score =  -2.40, R)
>droYak2.chrX 7667923 89 - 21770863
CGAGUCUAGCGAAUG-AGCCCAGAACUUGUGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAAAAAUGG-AAA---------------------
(((((((.((.....-.))..)).))))).((((((........)))))).(((((((.....))))))).................-...--------------------- ( -25.20, z-score =  -2.63, R)
>droEre2.scaffold_4690 16155045 111 + 18748788
CGAAUCCAGCGAACGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAAAAAGAA-AAAAUUACUGGCUGUACGUAGUAA
........(((.((((...((((.......((((((........)))))).(((((((.....))))))).................-.......)))))))).)))..... ( -30.80, z-score =  -2.97, R)
>dp4.chrXL_group1e 11211951 111 + 12523060
CAAAUCCGCCGGAUGGAGUCCAGAACUUGCGGUCACUGAUUCAUGCGGCCGGGGCUCUGGUCUGGGGUUCGGAUUUGGGAUACGGGU-CCGUUCUUUGGAUAUGGAUAGAGA
((.((((.(((((((((((((........(((((.(........).)))))))))))).))))))((..((((((((.....)))))-)))..))..)))).))........ ( -40.60, z-score =  -0.78, R)
>droPer1.super_14 655153 111 + 2168203
CAAAUCCGCCGGAUGGAGUCCAGAACUUGCGGUCACUGAUUCAUGCGGCCGGGGUUCUGGUCUGGGGUUCGGAUUUGGGAUACGGGU-CCGUUCUUUGGAUAUGGAUAGAGA
...(((((...........(((((((((.(((((.(........).))))))))))))))((..(((..((((((((.....)))))-)))..)))..))..)))))..... ( -42.90, z-score =  -1.66, R)
>consensus
CGAAUCCGGCGGAUGGAACCCAGAACUUGCGGUCACUGAUUCAUGUGAUCCCCAUCCCGAAAUGGGAUGGAAACAAAAAAAAAAGG__UAACUGGCUAGACGUACAA_____
....(((.......))).............((((((........)))))).(((((((.....))))))).......................................... (-18.73 = -17.03 +  -1.70)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,248,881 – 7,248,988
Length 107
Sequences 7
Columns 112
Reading direction reverse
Mean pairwise identity 66.93
Shannon entropy 0.63868
G+C content 0.47428
Mean single sequence MFE -27.94
Consensus MFE -16.04
Energy contribution -16.60
Covariance contribution 0.56
Combinations/Pair 1.32
Mean z-score -1.78
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.79
SVM RNA-class probability 0.995359
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 7248881 107 - 22422827
-----UUAUACGUAUAGCCAGUUAUUUUUUUUUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGUAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCAUCCGCAGGAUUCG
-----...........((..((((((..(((......((..((((((((.....))))))))...))...)))..)))))).)).(((((((((......)).))))))).. ( -26.70, z-score =  -2.22, R)
>droSim1.chrX 5785564 100 - 17042790
-----UUAUACGUAUAGCCAGUUA-------UUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCAUCCGCCGGAUUCG
-----............((((...-------....(((((..(((((((.....)))))))((.((((........)))))))))))..))))..(((.......))).... ( -26.60, z-score =  -0.98, R)
>droSec1.super_24 458486 100 - 912625
-----UUGUACGUAUAGCCAGUUA-------UUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCAUCCGCGGGAUUCG
-----...........((..((((-------((..(((((..(((((((.....)))))))..)).....)))..)))))).)).......(((((((......))))))). ( -28.70, z-score =  -1.16, R)
>droYak2.chrX 7667923 89 + 21770863
---------------------UUU-CCAUUUUUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCACAAGUUCUGGGCU-CAUUCGCUAGACUCG
---------------------...-..........(((((..(((((((.....)))))))((.((((........))))))))))).(((((.(.-.....)))))).... ( -23.60, z-score =  -1.72, R)
>droEre2.scaffold_4690 16155045 111 - 18748788
UUACUACGUACAGCCAGUAAUUUU-UUCUUUUUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCGUUCGCUGGAUUCG
......((.....(((((......-.............((..(((((((.....)))))))..)).....(((((...((.(....).))..))))).....)))))...)) ( -30.80, z-score =  -2.27, R)
>dp4.chrXL_group1e 11211951 111 - 12523060
UCUCUAUCCAUAUCCAAAGAACGG-ACCCGUAUCCCAAAUCCGAACCCCAGACCAGAGCCCCGGCCGCAUGAAUCAGUGACCGCAAGUUCUGGACUCCAUCCGGCGGAUUUG
....................(((.-...)))....((((((((.........(((((((..(((.(((........))).)))...)))))))...((....)))))))))) ( -29.60, z-score =  -1.88, R)
>droPer1.super_14 655153 111 - 2168203
UCUCUAUCCAUAUCCAAAGAACGG-ACCCGUAUCCCAAAUCCGAACCCCAGACCAGAACCCCGGCCGCAUGAAUCAGUGACCGCAAGUUCUGGACUCCAUCCGGCGGAUUUG
....................(((.-...)))....((((((((.........(((((((..(((.(((........))).)))...)))))))...((....)))))))))) ( -29.60, z-score =  -2.21, R)
>consensus
_____AUAUACAUACAGCCAGUUA__CCUUUUUUUUUUGUUUCCAUCCCAUUUCGGGAUGGGGAUCACAUGAAUCAGUGACCGCAAGUUCUGGGUUCCAUCCGCCGGAUUCG
......................................(((((((((((.....))))))))))).....(((((...((.(....).)).(((.....)))....))))). (-16.04 = -16.60 +   0.56)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:23:09 2011